rs9880088

Variant names:

• chr3-49141557-G-A
• rs9880088
• ENST00000603877.1:n.1723+620C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000603877.1(LAMB2P1):​n.1723+620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 151,918 control chromosomes in the GnomAD database, including 743 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.094 (743 hom., cov: 32)
• Consequence: LAMB2P1 ENST00000603877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 18 publications found

Genes affected

LAMB2P1 (HGNC:6488): (laminin subunit beta 2 pseudogene 1)

ENSG00000300884 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMB2P1	ENST00000603877.1	n.1723+620C>T		intron_variant	Intron 13 of 13	6
ENSG00000300884	ENST00000774820.1	n.82-6706G>A		intron_variant	Intron 1 of 1
ENSG00000300884	ENST00000774821.1	n.*207G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14239 AN: 151800 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0977

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0937 AC: 14240 AN: 151918 Hom.: 743 Cov.: 32 AF XY: 0.0933 AC XY: 6924 AN XY: 74216

African (AFR) AF: 0.0834 AC: 3456 AN: 41422

American (AMR) AF: 0.0775 AC: 1182 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3468

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5162

South Asian (SAS) AF: 0.0622 AC: 299 AN: 4810

European-Finnish (FIN) AF: 0.115 AC: 1211 AN: 10540

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7152 AN: 67944

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.0989 Hom.: 419

Bravo AF: 0.0900

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.50
PhyloP100		-0.033

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9880088; hg19: chr3-49178990;